OK, I will tell you up right here right now as you are having trouble, but use the sticky for future reference.

I understand you know how to get to the aircraft section of the FS9 main folder, so we will start there. It seems we are all missing the aircraft.cfg modification part of installing repaints... not a mention of it in this thread. Hmm...
Installing a repaint ALSO requires a modification of the aircraft.cfg file (not the .air file, mind you). Open the aircraft.cfg file, copy-paste this text, modifying it based on the name of the folder your new textures are in (Get rid of the text in parenthesis, by the way):
[fltsim.0,1,2, etc.] Check to see how many textures your plane already has, this number will be the next one after the last one.
title=XXX (This doesn't really matter much, but change it so you know which specific aircraft this block of code is referring to)
sim=747-400-RR-RB-211-524HT (This MUST match the sim code of the currently working aircraft, else the textures won't be detected)
model=RR (Only needed if your plane has several different model folders, this will make the program use that model to map the textures to)
panel= (If you want a different panel in your aircraft, remove the panel folder and either re-map here, or in the panel.cfg file)
sound= (Use this to re-map the sounds this plane will use, can also be done in the sound.cfg file)
texture=SAF (This one is ESSENTIAL to texture modification, insert the text on the RIGHT side of the dot [ex: texture.(FedEx) (insert this one)] in this field so the plane will read the textures in that specific folder.)
checklists= (Not essential)
atc_airline=Springbok (this changes the airline that ATC will refer to you as, not essential)
atc_flight_number=201 (This simply changes the default flight number ATC registers you as, not really important)
ui_manufacturer=Boeing (This re-categorizes the plane in the select aircraft menu, I change this one a lot to keep all my Boeing aircraft under "Boeing")
ui_type=747-400 (This is what the actual name of the plane will be in aircraft select)
ui_variation=South African Airways (This MUST be changed in order to insert a repaint into a plane, you will find this in the variation dropdown in aircraft select)
visual_damage=1 (Not essential)
atc_heavy=1 (Tells ATC whether or not your plane is a "heavy" not essential)
atc_id=ZS-SAY1 (ATC Tailnumber reference)
description= Say what you want to say about the plane here.
Hope this helps.

By the way, whenever you download a repaint, most come with the above coding already prepared. This should help you with those that don't. If the repaint comes with an aircraft.cfg modification, all you really need to do is insert it into the plane's aircraft.cfg, modify the fltsim.XXX, and sometimes the sim=, and then you are ready to go.